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Data Store Guide

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Goal

The Data Store is more than having a place to save your files. The Data Store is a way to manage the life cycle of your data. From the moment you create data, to publication and beyond, there are a number of practices you should follow to ensure the integrity and value of your data are maintained. This includes making your data FAIR (Findable, Accessible, Interoperable, and Reusable). The Data Store helps to achieve this with less effort. This guide will cover the minimum needed to get you started. Please look through the Data Store Manual for a more comprehensive look at Data Store capabilities.

Maintainer	Institution	Contact
Jason Williams	CyVerse / CSHL	Williams@cshl.edu

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• Tutorial home
• Drag-and-drop Data Transfer with Cyberduck
  • Download and first-time configuration of Cyberduck
  • Upload from local computer to Data Store using Cyberduck
  • Download from Data Store to local computer using Cyberduck
• Command Line Transfer with iCommands
  • iCommands Installation for Linux
  • iCommands Installation for Mac OS X
  • iCommands First-time Configuration
  • Anonymous access to the CyVerse Datastore
  • Upload Files/folders from local Computer to Data Store
  • Download Files/folders from Data Store to local Computer
  • NetCDF iCommands
  • Additional Frequently Used iCommands
• Associate Data with Metadata
  • Viewing and Editing Metadata for a Single File/folder in the Discovery Environment
  • Adding Metadata to Multiple Files/folder in the Discovery Environment
• Data Sharing and Other Features
  • Share a File in Discovery Environment with a URL (Public Link)
  • Share a File/folder in Discovery Environment with Another CyVerse User
• Desktop Access with WebDav
  • Limitations
  • Accessing CyVerse data via WebDAV Services
  • User Data
  • Community Released Data/Project Data
  • CyVerse Curated Data (Data with a DOI)
  • Common Ways to Access the WebDAV Service
  • Summary

Prerequisites

Downloads, access, and services

In order to complete this tutorial you will need access to the following services/software

Prerequisite	Preparation/Notes	Link/Download
CyVerse account (optional)	CyVerse supports anonymous data access to public data sets in the CyVerse Data Commons. This guide is written with the assumption you are a CyVerse account holder. See the Data Store Manual for more info on anonymous access.	Register: CyVerse User Portal
Cyberduck (optional)	Cyberduck is a 3rd party application with a graphical user interface that allows you to easily upload and download data. (available for Mac /PC). You will also need to download our connection profile (bookmark).	Cyberduck Website Cyberduck connection profile
iCommands (optional)	iCommands are a set of command line binaries that can be used to interact with the Data Store. Download iCommands (available for Mac/ Linux) if you want to use these functionalities.	iCommands (for Mac) Mac OS iCommands Download iCommands (for Linux; see iCommands CLI) Linux CLI iCommands Download
Spreadsheet editor (optional)	To edit a metadata template in .csv format, we recommend using a spreadsheet editor such as Microsoft Excel or LibreOffice Calc.	Free LibreOffice

Warning

When uploading your data to the Data Store you should not upload files/folders with names containing spaces (e.g. experiment one.fastq) or name that contain special characters (e.g. ~ ` ! @ # $ % ^ & * ( ) + = { } [ ] | : ; ” ‘ < > , ? /). The Apps on the Discovery Environment and most command line apps will typically not tolerate these characters. For long file/folder names the use of underscores (e.g. experiment_one.fastq) is the recommended practice.

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